Using Next Generation Sequencing for Tagging Positive Genes from S. spontaneum

S. spontaneum provides sugarcane researchers with a valuable genetic resource to improve the genetic traits of commercial sugarcane hybrids. Especially, abiotic stress tolerance (e.g. cold, drought) is of great interest among sugarcane breeders. Our lab compared the gene expression profiles, by RNA-seq, between a commercial sugarcane hybrid (CP72-1210, cold susceptible) and a cold tolerant genotype of S. spontaneum (TUS05-05), before and after cold stress, in order to investigate the gene(s) contributing cold stress tolerance in S. spontaneum. RNA-seq data showed that the major differences in the gene expression profiles between the cold susceptible and tolerant genotypes are in those genes with catalytic and binding activities. Based on the RNA-seq data, we have selected seven genes for further study from a list of genes that are induced after cold stress. Real-time quantitative PCR (RT-qPCR) data confirmed that four of those seven genes are consistently induced after cold stress. Our working hypothesis is that a specific protein, encoded by the contig detected, is induced in TUS05-05 by cold stress, but in lower intensity in CP72-1210, which activates transcription factor(s), leading to the expression of genes related to cold tolerance in TUS05-05. Currently, plant transformation is in progress, in order to investigate the functionality of each of those genes in cold stress tolerance.  In addition, a Bacterial Artificial Chromosome library from TUS05-5 in being constructed to allow the identification of the promoter sequences involved.